Changes

Generate XDS.INP (view source)

Revision as of 07:40, 10 April 2016

2,330 bytes added , 07:40, 10 April 2016

rev 0.6.1 (tentative Eiger hdf5 support using h5dump)

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# revision 0.59 . KD 04/04/2016 check for ADSC detector _after_ checking for dtrek detector, to correct wrong choice for https://zenodo.org/record/45756

# revision 0.60 . KD 04/04/2016 ADSC detector SN=458 at APS 19-ID has reverse phi (https://zenodo.org/record/45756)

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REVISION="0.60 (04-Apr-2016)"

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# revision 0.61 . Keitaro 10/04/2016 Add Eiger hdf5 support (may be incomplete; UNTRUSTED_RECTANGLE=s not set) NEED h5dump.

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REVISION="0.61 (10-Apr-2016)"

#

# usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img"

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spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l`

SPOT_RANGE="$data_first $spot_last"

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FIRSTFRAME=`head -1 tmp1`

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echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0

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if [ "$is_h5" == 1 ]; then

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nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'`

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DATA_RANGE="1 $nframes"

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SPOT_RANGE="1 `echo "scale=0; ${nframes}/2"|bc -l`"

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fi

echo DATA_RANGE=$DATA_RANGE

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DET=XXX

IFS=$'\n'

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~~FIRSTFRAME=`head -1 tmp1`~~

echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1

# for mac/linux compatibility. zcat foo.gz doesn't work on mac.

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echo $FIRSTFRAME | grep -q '\.xz$' && xzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1

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~~strings $FIRSTFRAME > tmp2~~

unset IFS

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# TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead

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if [ "$is_h5" == 0 ]; then

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# this was done for "mccd", but still has to be done for the "raxis" detector types

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strings $FIRSTFRAME > tmp2

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# the reason is that FIRSTFRAME may contain a blank, which makes some commands fail

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# TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead

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egrep -qi 'marccd|Corrected' tmp2 && DET=mccd

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# this was done for "mccd", but still has to be done for the "raxis" detector types

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grep -q PILATUS tmp2 && DET=pilatus

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# the reason is that FIRSTFRAME may contain a blank, which makes some commands fail

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head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis

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egrep -qi 'marccd|Corrected' tmp2 && DET=mccd

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head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis

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grep -q PILATUS tmp2 && DET=pilatus

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grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek

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head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis

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grep -q BEAM_CENTER_X tmp2 && DET=adsc

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head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis

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grep -q mar345 tmp2 && DET=MAR345

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grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek

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grep -q BEAM_CENTER_X tmp2 && DET=adsc

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grep -q mar345 tmp2 && DET=MAR345

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else

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h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger

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fi

# identify other detector types in the same way

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fi

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elif [ "$DET" == "eiger" ]; then

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OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/$0$:/{print $2}' `

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DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !EIGER"

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QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2*1000}'`

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QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2*1000}'`

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echo Data from a Eiger hdf5

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SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2*1000}'`

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X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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NX=`h5dump -d "/entry/instrument/detector/detectorSpecific/x_pixels_in_detector" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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NY=`h5dump -d "/entry/instrument/detector/detectorSpecific/y_pixels_in_detector" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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# find ORGX and ORGY:

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ORGX=`h5dump -d "/entry/instrument/detector/beam_center_x" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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# find DETECTOR_DISTANCE and OSCILLATION_RANGE:

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DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2*1000}'`

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OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/$0$: [0-9]/{print $2}'`

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# If rotation vector set (NeXus)

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rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"`

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elif [ "$DET" == "raxis" ]; then

echo Data from a RAXIS detector

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rotx=`echo "scale=6; -1.0*${tmpmat[0]}" | bc -l`

roty=`echo "scale=6; -1.0*${tmpmat[1]}" | bc -l`

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~~dtrek_rotation_axis~~="$rotx $roty 0"

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rotation_axis="$rotx $roty 0"

if [ `echo "(${tmpmat[0]}*${tmpmat[3]}-(${tmpmat[1]}*${tmpmat[2]}))/1"|bc` -lt 0 ]; then

echo ""

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eof

else

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if [ "$~~dtrek_rotation_axis~~" != "" ]; then

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if [ "$rotation_axis" != "" ]; then

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echo "ROTATION_AXIS= $~~dtrek_rotation_axis~~" >> XDS.INP

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echo "ROTATION_AXIS= $rotation_axis" >> XDS.INP

elif [ "$REVERSE_PHI" == "no" ]; then

echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP

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!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak

eof

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if [ "$DET" == "pilatus" ]; then

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if [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then

cat >> XDS.INP << eof

SEPMIN=4 CLUSTER_RADIUS=2

Keitaro

33

edits